From b231a40da5b0c282cc76fb6146478c80f23e1544 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 Apr 2011 13:42:48 +0000
Subject: [PATCH] Augment PrintLocusContextWalker with extended event info.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5583 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/qc/PrintLocusContextWalker.java   | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
index f26f40a6a..39b69ba29 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
@@ -21,12 +21,15 @@ public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integ
     private PrintStream out;
 
     public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBaseAsChar(),
-                                                                context.getLocation(),
-                                                                Arrays.deepToString( getReadNames(context.getReads()) ) );
+        out.printf( "In map: ref = %s, loc = %s %s, reads = %s%n", ref.getBaseAsChar(),
+                                                                   context.getLocation(),
+                                                                   context.hasExtendedEventPileup() ? "[extended]" : "",
+                                                                   Arrays.deepToString( getReadNames(context.getReads()) ) );
         return context;
     }
 
+
+
     public Integer reduceInit() { return 0; }
 
     public Integer reduce(AlignmentContext context, Integer sum) {
@@ -45,4 +48,9 @@ public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integ
         //Arrays.sort(readNames);
         return readNames;
     }
+
+    @Override
+    public boolean generateExtendedEvents() {
+        return true;
+    }    
 }